Functions — github.com/bytedance/dplm

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Functions1,008 in github.com/bytedance/dplm

⨍ Functions 1,008◇ Types & classes 149↳ Endpoints 2

↓ 2 callersFunctionremove_lowconf_ends

(row, threshold=50)

src/byprot/datamodules/dataset/tokenized_protein.py:29

↓ 2 callersFunctionsample_from_categorical

(logits=None, temperature=1.0)

src/byprot/models/utils.py:325

↓ 2 callersFunctionsave_results

( tokenizer, struct_tokenizer, save_dir, task, outputs, headers=None, save_pdb=Tru

generate_dplm2.py:354

↓ 2 callersFunctionscore_fun8

1, collect those residues with dis<d; 2, calculate TMscore

analysis/TMalign.cpp:1719

↓ 2 callersFunctionscore_fun8_standard

analysis/TMalign.cpp:1762

↓ 2 callersFunctionstandard_TMscore

analysis/TMalign.cpp:3787

↓ 2 callersMethodstep

batch is a Dict containing: - corrds: FloatTensor [bsz, len, n_atoms, 3], coordinates of proteins - corrd_mask: BooltTensor [bsz, len

src/byprot/tasks/lm/dplm.py:101

↓ 2 callersMethodstep

batch is a Dict containing: - corrds: FloatTensor [bsz, len, n_atoms, 3], coordinates of proteins - corrd_mask: BooltTensor [bsz, len

src/byprot/tasks/lm/mlm.py:157

↓ 2 callersMethodstep

batch is a Dict containing: - corrds: FloatTensor [bsz, len, n_atoms, 3], coordinates of proteins - corrd_mask: BooltTensor [bsz, len

src/byprot/tasks/lm/dplm2.py:127

↓ 2 callersMethodstep

batch is a Dict containing: - corrds: FloatTensor [bsz, len, n_atoms, 3], coordinates of proteins - corrd_mask: BooltTensor [bsz, len

src/byprot/tasks/lm/dplm_invfold.py:232

↓ 2 callersMethodstep

(self, batch)

src/byprot/tasks/struct_tokenizer/structok.py:142

↓ 2 callersMethodstring_to_tensor

(self, aatype_str, struct_token_str)

src/byprot/models/structok/structok_lfq.py:257

↓ 2 callersFunctiontm_set2set

(querys, targets, save_path, n_threads=mp.cpu_count())

analysis/cal_tmscore.py:60

↓ 2 callersMethodtokenize

(self, atom_positions, res_mask, seq_length=None)

src/byprot/models/structok/structok_lfq.py:214

↓ 2 callersFunctiontopk_masking_prior

scores: [b, n] cutoff_len: [b, 1] stochastic: bool, whether to add noise to select top_k or not returns: mask: [b, n], with 1

src/byprot/models/utils.py:278

↓ 2 callersFunctiontorsion_angles_to_frames

Conversion method of torsion angles to frames provided the backbone. Args: r: Backbone rigid groups. alpha: Torsion angles.

src/byprot/utils/protein/all_atom.py:53

↓ 1 callersFunctionCPalign_main

entry function for TM-align with circular permutation * i_opt, a_opt, u_opt, d_opt, TMcut are not implemented yet */

analysis/TMalign.cpp:4528

↓ 1 callersFunctionNWalign_main

entry function for NWalign * invmap_only - whether to return seqxA and seqyA or to return invmap * 0: only return seqxA and seqyA

analysis/TMscore.cpp:3995

↓ 1 callersFunctionTMscore_main

Entry function for TM-score. Return TM-score calculation status: * 0 - full TM-score calculation * 1 - terminated due to exception * 2-7 -

analysis/TMscore.cpp:6315

↓ 1 callersFunctionToPiFoldFormat

(X, S, cfd, pad_special_tokens=False)

src/byprot/datamodules/dataset/cath.py:390

↓ 1 callersMethod__call__

Args: raw_batch: List of tuples (coords, confidence, seq) In each tuple, coords: list of floats, shap

src/byprot/datamodules/dataset/cath.py:203

↓ 1 callersMethod__call__

(self, raw_batch: dict)

src/byprot/datamodules/dataset/cath.py:428

↓ 1 callersMethod__init__

(self)

src/byprot/tasks/__init__.py:262

↓ 1 callersMethod__init__

(self, config=None)

src/byprot/models/structok/modules/loss.py:1773

↓ 1 callersMethod__init__

(self, alphabet=None, freeze=True, return_logits=False)

src/byprot/models/structok/modules/gvp_encoder.py:15

↓ 1 callersMethod__init__

(self, **kwargs)

src/byprot/models/structok/modules/folding_utils/trunk.py:119

↓ 1 callersMethod__init__

(self, dataset: Dataset[T_co], indices: Sequence[int])

src/byprot/datamodules/dataset/uniref.py:244

↓ 1 callersMethod__init__

( self, name="esm", featurizer="cath", alphabet_cfg={}, featurizer_cfg={} )

src/byprot/datamodules/dataset/data_utils.py:29

↓ 1 callersMethod__init__

(self, dataset: Dataset[T_co], indices: Sequence[int])

src/byprot/datamodules/dataset/uniref_hf.py:252

↓ 1 callersMethod__init__

( self, alphabet: Alphabet, to_pifold_format=False, coord_nan_to_zero=True,

src/byprot/datamodules/dataset/cath.py:411

↓ 1 callersMethod_af2_idx_to_esm_idx

(self, aa, mask)

src/byprot/models/structok/modules/folding_utils/decoder.py:137

↓ 1 callersMethod_af2_idx_to_esm_idx

(self, aa, mask)

src/byprot/models/structok/modules/folding_utils/esmfold.py:113

↓ 1 callersMethod_af2_model

(self, fasta_path, output_dir)

src/byprot/utils/protein/folding_model.py:86

↓ 1 callersMethod_af2_to_esm

(d: Alphabet)

src/byprot/models/structok/modules/folding_utils/decoder.py:130

↓ 1 callersMethod_af2_to_esm

(d: Alphabet)

src/byprot/models/structok/modules/folding_utils/esmfold.py:106

↓ 1 callersMethod_build

(self)

src/byprot/modules/__init__.py:22

↓ 1 callersMethod_build_batch_sampler

( self, dataset, max_tokens, shuffle=False, distributed=True )

src/byprot/datamodules/pdb_dataset/pdb_datamodule.py:153

↓ 1 callersMethod_build_batches

(self)

src/byprot/datamodules/dataset/data_utils.py:424

↓ 1 callersMethod_build_batches

(self)

src/byprot/datamodules/dataset/tokenized_protein.py:189

↓ 1 callersMethod_build_batches

(self)

src/byprot/datamodules/dataset/uniref_hf.py:110

↓ 1 callersFunction_calculate_expected_aligned_error

( alignment_confidence_breaks: torch.Tensor, aligned_distance_error_probs: torch.Tensor, )

src/byprot/models/structok/modules/loss.py:669

↓ 1 callersFunction_compare_version

Compare package version with some requirements. >>> _compare_version("torch", operator.ge, "0.1") True >>> _compare_version("does_not_exi

src/byprot/utils/callbacks.py:43

↓ 1 callersMethod_compute_input_representations

(self, emb_s, emb_z, esmaa)

src/byprot/models/structok/modules/folding_utils/decoder.py:176

↓ 1 callersMethod_compute_language_model_representations

Adds bos/eos tokens for the language model, since the structure module doesn't use these.

src/byprot/models/structok/modules/folding_utils/esmfold.py:117

↓ 1 callersMethod_compute_validation_metrics

( self, batch, outputs, superimposition_metrics=False )

src/byprot/tasks/struct_tokenizer/structok.py:263

↓ 1 callersFunction_convert_target_to_string

(t: Any)

src/byprot/utils/config.py:102

↓ 1 callersMethod_esmf_model

(self, fasta_path, output_dir)

src/byprot/utils/protein/folding_model.py:57

↓ 1 callersFunction_make_rigid_group_constants

Fill the arrays above.

src/byprot/utils/protein/residue_constants.py:1136

↓ 1 callersFunction_make_rigid_group_constants

Fill the arrays above.

src/byprot/datamodules/pdb_dataset/residue_constants.py:1136

↓ 1 callersFunction_make_standard_atom_mask

Returns [num_res_types, num_atom_types] mask array.

src/byprot/utils/protein/residue_constants.py:1040

↓ 1 callersFunction_make_standard_atom_mask

Returns [num_res_types, num_atom_types] mask array.

src/byprot/datamodules/pdb_dataset/residue_constants.py:1040

↓ 1 callersMethod_map_aatypes

(self, tokens)

src/byprot/datamodules/dataset/cath.py:352

↓ 1 callersMethod_mask_inputs_to_esm

(self, esmaa, pattern)

src/byprot/models/structok/modules/folding_utils/decoder.py:180

↓ 1 callersMethod_mask_inputs_to_esm

(self, esmaa, pattern)

src/byprot/models/structok/modules/folding_utils/esmfold.py:142

↓ 1 callersFunction_package_available

Check if a package is available in your environment. >>> _package_available('os') True >>> _package_available('bla') False

src/byprot/utils/callbacks.py:29

↓ 1 callersMethod_post_quant

(x, mask)

src/byprot/models/structok/structok_lfq.py:162

↓ 1 callersMethod_prepare_special_token

(self)

src/byprot/models/dplm2/dplm2_bit.py:80

↓ 1 callersMethod_prepare_special_token

(self)

src/byprot/models/dplm2/dplm2.py:168

↓ 1 callersMethod_process_csv_row

(self, csv_row)

src/byprot/datamodules/pdb_dataset/pdb_datamodule.py:522

↓ 1 callersMethod_reparam_decoding

This function is used to perform reparameterized decoding.

src/byprot/models/dplm/dplm.py:387

↓ 1 callersMethod_reparam_decoding

This function is used to perform reparameterized decoding.

src/byprot/models/dplm/dplm_invfold.py:283

↓ 1 callersMethod_replica_epoch_batches

(self)

src/byprot/datamodules/pdb_dataset/pdb_datamodule.py:610

↓ 1 callersFunction_rog_quantile_curve

(df, quantile, eval_x)

src/byprot/datamodules/pdb_dataset/pdb_datamodule.py:677

↓ 1 callersMethod_run_struct_tokenizer

(self, batch, output_dir, is_trajectory=False)

src/byprot/utils/protein/evaluator_dplm2.py:288

↓ 1 callersMethod_update_cfg

(self, cfg)

src/byprot/models/dplm/dplm.py:106

↓ 1 callersMethod_update_cfg

(self, cfg)

src/byprot/models/dplm/dplm_invfold.py:61

↓ 1 callersMethod_update_cfg

(self, cfg)

src/byprot/models/dplm/modules/dplm_adapter.py:146

↓ 1 callersMethod_update_cos_sin_tables

(self, x, type_ids, seq_dimension=2)

src/byprot/models/dplm2/modules/dplm2_modeling_esm.py:40

↓ 1 callersMethod_update_cos_sin_tables

(self, x, type_ids, seq_dimension=2)

src/byprot/models/dplm2/modules/dplm2_bit_modeling_esm.py:40

↓ 1 callersMethodadapter_feed_forward_chunk

(self, attention_output)

src/byprot/models/dplm/modules/dplm_adapter.py:282

↓ 1 callersFunctionadd_diversity_metrics

(designable_dir, designable_csv, designable_csv_path)

src/byprot/utils/protein/utils.py:171

↓ 1 callersFunctionadjust_oxygen_pos

Imputes the position of the oxygen atom on the backbone by using adjacent frame information. Specifically, we say that the oxygen atom is in t

src/byprot/utils/protein/all_atom.py:294

↓ 1 callersFunctionadjust_oxygen_pos

Imputes the position of the oxygen atom on the backbone by using adjacent frame information. Specifically, we say that the oxygen atom is in t

src/byprot/datamodules/pdb_dataset/all_atom.py:294

↓ 1 callersFunctionapprox_TM

calculate approximate TM-score given rotation matrix */

analysis/TMscore.cpp:5748

↓ 1 callersFunctionatom37_from_trans_rot

(trans, rots, res_mask)

src/byprot/utils/protein/all_atom.py:270

↓ 1 callersFunctionatom37_from_trans_rot

(trans, rots, res_mask)

src/byprot/datamodules/pdb_dataset/all_atom.py:270

↓ 1 callersFunctionbackbone_loss

( backbone_rigid_tensor: torch.Tensor, backbone_rigid_mask: torch.Tensor, traj: torch.Tensor,

src/byprot/models/structok/modules/loss.py:247

↓ 1 callersFunctionbetween_residue_bond_loss

Flat-bottom loss to penalize structural violations between residues. This is a loss penalizing any violation of the geometry around the peptide

src/byprot/models/structok/modules/loss.py:811

↓ 1 callersFunctionbetween_residue_clash_loss

Loss to penalize steric clashes between residues. This is a loss penalizing any steric clashes due to non bonded atoms in different peptides

src/byprot/models/structok/modules/loss.py:976

↓ 1 callersMethodbuild_criterion

(self)

src/byprot/tasks/lm/dplm.py:89

↓ 1 callersMethodbuild_criterion

(self)

src/byprot/tasks/lm/mlm.py:93

↓ 1 callersMethodbuild_criterion

(self)

src/byprot/tasks/lm/dplm2.py:94

↓ 1 callersMethodbuild_criterion

(self)

src/byprot/tasks/lm/dplm_invfold.py:141

↓ 1 callersMethodbuild_criterion

(self)

src/byprot/tasks/struct_tokenizer/structok.py:117

↓ 1 callersMethodbuild_generator

(self)

src/byprot/tasks/lm/dplm_invfold.py:134

↓ 1 callersMethodbuild_model

(self)

src/byprot/tasks/lm/dplm.py:83

↓ 1 callersMethodbuild_model

(self)

src/byprot/tasks/lm/mlm.py:89

↓ 1 callersMethodbuild_model

(self)

src/byprot/tasks/lm/dplm2.py:88

↓ 1 callersMethodbuild_model

(self)

src/byprot/tasks/lm/dplm_invfold.py:128

↓ 1 callersMethodbuild_model

(self)

src/byprot/tasks/struct_tokenizer/structok.py:111

↓ 1 callersMethodbuild_torchmetric

(self)

src/byprot/tasks/lm/dplm.py:95

↓ 1 callersMethodbuild_torchmetric

(self)

src/byprot/tasks/lm/mlm.py:99

↓ 1 callersMethodbuild_torchmetric

(self)

src/byprot/tasks/lm/dplm2.py:100

↓ 1 callersMethodbuild_torchmetric

(self)

src/byprot/tasks/lm/dplm_invfold.py:147

↓ 1 callersMethodbuild_torchmetric

(self)

src/byprot/tasks/struct_tokenizer/structok.py:122

↓ 1 callersFunctionca_ca_clashes

(ca_pos, tol=1.5)

src/byprot/modules/protein_metrics.py:214

↓ 1 callersFunctionca_ca_distance

(ca_pos, tol=0.1)

src/byprot/modules/protein_metrics.py:205

↓ 1 callersFunctioncal_diversity

(query_dir, reference_dir)

analysis/cal_tmscore.py:133

↓ 1 callersFunctioncal_novelty

(query_dir, reference_dir)

analysis/cal_tmscore.py:111

↓ 1 callersFunctioncalc_mdtraj_metrics

(pdb_path)

src/byprot/modules/protein_metrics.py:79

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